Perform Positional Analogue Scanning using the SMILES Manager Element

Hello, In this tutorial, I will show you how to run a simple but powerful technique, called positional analogue scanning, in order to generate new analogs of your molecules directly in SAMSON using the SMILES Manager element. This new functionality was inspired by this blog post from Pat Walters and this paper from Lewis Pennington, Ingo Muegge, and coworkers. It will allow you to evaluate the effects of newly introduced changes of your molecules on their properties, like the binding affinity (using Autodock…

More…

Computing normal modes that open a binding site

Hello all, Welcome to this tutorial, I will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Element. This SAMSON Element computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the NMAL module and indicate the desired…

More…

GROMACS Wizard

In this tutorial I will present you GROMACS Wizard Element, a new SAMSON element for system preparation and simulation using the well-known GROMACS package. With GROMACS Wizard Element, the main GROMACS features are now integrated into SAMSON. For example, it will help you to easily run GROMACS simulations and get results as plots and simulation trajectories. Moreover, you will not have to compile/install the GROMACS package itself as this module comes with the GROMACS version 5.1 already installed. In addition, this module…

More…

Using the RDKit – SMILES Manager

Hello everyone, In this post I will present you the new version of the RDKit-SMILES Manager module that I integrated in the SAMSON platform. As some of you know, RDKit is an open-source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules SMILES strings to a 2D and 3D structures. The module interface presents two tabulations: Manage SMILES and Replace fragments. I will present these two sections one by one as…

More…

Calculating non-linear normal modes

Hello all, Welcome to this tutorial, I will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Element. This SAMSON Element is an advanced version of the Normal Modes Analysis SAMSON Element also available on SAMSON Connect. This SAMSON Element computes nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a…

More…

Computing non-linear normal modes of biomolecules

Hello all, Welcome to this tutorial. Here, I will present you the functionalities of the Normal Modes Analysis Lite (NMAL) SAMSON Element. This SAMSON Element computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021 / acs.jctc.7b00197.). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the…

More…